MBD6
protein-codingmethyl-CpG binding domain protein 6, the group of Methyl-CpG binding domain containing
Gene summary
Enables chromatin binding activity. Located in chromocenter and nucleoplasm. Implicated in autism spectrum disorder. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MBD6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_052897.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 8 | 2 | 10 | |||
| missense | 170 | 9 | 3 | 182 | ||
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 181 | 17 | 5 | 203 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_443129.3 | 11 | MANE Select | |
| Ensembl | ENSP00000347896.3 | 11 | MANE Select | |
| Ensembl | ENSP00000448202.1 | 2 | Standard | |
| Ensembl | ENSP00000449603.1 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| mbd6 | Danio rerio | Structure: definitive hemopoiesis Quality: increased occurrence abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Post-translational protein modification
- Metabolism of proteins
- UCH proteinases
- Deubiquitination
Biological Process
- protein deubiquitination
Molecular Function
- DNA binding
- chromatin binding
Cellular Component
- fibrillar center
- nucleus
- nucleoplasm
- chromocenter
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000355673
- Coding exons
- 11
- Length
- 9439
- Individuals with no LoFs
- 125735
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125748
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.741 | 628 | 578 | 1.09 | 0.0000322 | 6190 |
| Missense (PolyPhen) | 66 | 48.63 | 1.3572 | 380 | ||
| Synonymous | 0.198 | 234 | 238 | 0.984 | 0.0000122 | 2466 |
| Loss of Function | 4.74 | 2 | 30.1 | 0.0665 | 0.00000172 | 336 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00012 | rare |
| Latino/Admixed American | 0.000060 | 0.000058 | rare |
| Ashkenazi Jewish | 0.00011 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000073 | 0.000070 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Binds to heterochromatin. Does not interact with either methylated or unmethylated DNA (in vitro).;
Recessive Scores
- pRec
- 0.0998
Intolerance Scores
- LoFtool
- 0.0550
- RVIS EVS
- -1.46
- RVIS percentile EVS
- 3.82
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.803
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |